Abstract

Chromatin is probably the most complex molecular ensemble in the cell. It consists of genomic DNA bound by hundreds of protein and RNA molecules. All of these components work in concert, and cannot be fully understood unless they are studied in their complete context. In addition, the spatial organization of interphase chromosomes is thought to be of key importance for genome expression and maintenance. Yet, this three-dimensional chromosome organization and its impact on gene regulation and other functions are still poorly understood. In order to gain insight into these fundamental processes, we take a broad integrative genomics approach, using both fruit fly and mammalian cells as model systems. We conduct our studies in the living cell, in the context of the entire genome. We develop and apply new genomics techniques to reveal the interplay among many chromatin proteins, to visualize the architecture of chromosomes inside the nucleus, and to detect the genome-wide effects of these factors on gene expression. We analyze the large datasets that we generate using a range of bioinformatics approaches.